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ATRX Mutations in Neuroblastoma Are Associated with Poor Outcome and Age at Diagnosis

Neuroblastoma is a cancer of the developing sympathetic nervous system and accounts for 15% of all cancer-related deaths in children. It is one of the most enigmatic pediatric cancers because some patients respond very well to conventional therapy, whereas others fare much worse. Some patients even show spontaneous regression of neuroblastoma without any treatment at all.

For children with the most advanced form of metastatic neuroblastoma (stage 4), age at diagnosis is strongly associated with overall survival. For those younger than 18 months at diagnosis, the probability of overall survival is 88%; for those 18 months to 12 years, 49%; and for those older than 12 years, only 10%.

Dr. Michael A. Dyer and Alberto S. Pappo, MD (Oncology), co-leaders of the Developmental Biology & Solid Tumor Program of the St. Jude Comprehensive Cancer Center, hypothesized that genomic differences may account for this striking association between age and outcome for children with stage-4 neuroblastoma. To test this hypothesis, Drs. Dyer and Pappo initiated a collaboration with Dr. Nai-Kong Cheung at Memorial Sloan-Kettering Cancer Center (New York, NY), who has a unique collection of stage-4 neuroblastoma tumor samples from each age group.

Through the Pediatric Cancer Genome Project (PCGP), whole-genome sequencing was performed on the DNA from 40 stage-4 neuroblastoma tumors in a discovery group and an additional 64 tumors that were used for validation. Results of these and further analyses were published in the Journal of the American Medical Association.

Mutations in the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene were associated with age at diagnosis of stage-4 neuroblastoma across the 104 tumor samples. None of the very young children had tumors with ATRX mutations. Among those 18 months to 12 years of age, 17% had ATRX mutations, and among the adolescents and young adults, 44% had ATRX mutations.

To explore the biological consequences of ATRX mutations, Drs. Dyer and Pappo enlisted the expertise of Armita Bahrami, MD (Pathology). The ATRX protein is an important epigenetic regulator that contributes to chromatin remodeling and telomere maintenance. Dr. Bahrami showed that neuroblastoma cells with ATRX mutations lack the ATRX protein in their nuclei.

She then investigated the functional consequences of ATRX mutations by analyzing the telomeres. Matthew Parker, PhD (Computational Biology), had already shown that the telomeres in ATRX-mutant neuroblastomas are longer than those in neuroblastoma cells that do not express ATRX mutations by using whole-genome sequencing data and quantitative PCR. Using fluorescence in situ hybridization to study telomere organization in neuroblastomas, Dr. Bahrami demonstrated that ATRX-mutant neuroblastomas carry all the hallmarks of the unique mechanism of telomere maintenance called alternative lengthening of telomeres (ALT).

The DNA in telomeres at the end of chromosomes cannot be fully replicated during mitosis; therefore, with each cell cycle the telomeres become shorter, ultimately resulting in the senescence of cell division. In this manner, telomere attrition limits cell proliferation. However, ALT counteracts this attrition, thereby enabling cancer cells to continue to proliferate.

This study provides new insight into the biology of neuroblastoma and calls attention to the importance of epigenetic regulators in cancer progression. Beyond its role in maintaining the structure of telomeres, ATRX regulates the deposition of histone H3.3, a protein that regulates cell division and chromosome segregation, at transcriptionally silent regions of the genome.

These data suggest that neuroblastomas with ATRX mutations ectopically activate oncogenes that contribute to the poor outcome of older children with neuroblastoma. Drs. Dyer and Pappo and their collaborators at St. Jude and Memorial Sloan-Kettering Cancer Center are testing this hypothesis and working to advance our understanding of the role of epigenetics in neuroblastoma progression during phase II of the PCGP.